8Q3E

High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IPU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.168	α = 90
b = 109.638	β = 90
c = 183.557	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	98	PIXEL	DECTRIS PILATUS 2M-F		2018-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.04	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.17	48.852	98.2	1	20.3	12.2		112248

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.29			0.573

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.174	48.852	112016	2303	98.108	0.235	0.2343	0.2697	3	80.065

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.289			-3.34		2.051

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.454
r_dihedral_angle_4_deg	21.897
r_dihedral_angle_3_deg	19.019
r_lrange_it	13.674
r_lrange_other	13.674
r_scangle_it	10.622
r_scangle_other	10.621
r_mcangle_it	7.331
r_mcangle_other	7.33
r_scbond_it	7.263
r_scbond_other	7.261
r_dihedral_angle_1_deg	6.28
r_mcbond_it	5.277
r_mcbond_other	5.265
r_angle_refined_deg	1.511
r_angle_other_deg	1.49
r_symmetry_xyhbond_nbd_refined	0.298
r_nbd_other	0.234
r_symmetry_nbd_other	0.214
r_nbd_refined	0.206
r_nbtor_refined	0.206
r_symmetry_nbd_refined	0.185
r_xyhbond_nbd_refined	0.138
r_symmetry_xyhbond_nbd_other	0.093
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6257
Nucleic Acid Atoms	5939
Solvent Atoms
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing